Field Detail

• INPUT

  @Argument(shortName="I",
            doc="Input BAM file for analysis.")
  public File INPUT

• OUTPUT

  @Argument(shortName="O",
            doc="Location of output metrics file to write.")
  public File OUTPUT

• INTERVALS

  @Argument(doc="An optional list of intervals to restrict analysis to.",
            optional=true)
  public File INTERVALS

• DB_SNP

  @Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
            optional=true)
  public File DB_SNP

• MINIMUM_QUALITY_SCORE

  @Argument(shortName="Q",
            doc="The minimum base quality score for a base to be included in analysis.")
  public int MINIMUM_QUALITY_SCORE

• MINIMUM_MAPPING_QUALITY

  @Argument(shortName="MQ",
            doc="The minimum mapping quality score for a base to be included in analysis.")
  public int MINIMUM_MAPPING_QUALITY

• MINIMUM_INSERT_SIZE

  @Argument(shortName="MIN_INS",
            doc="The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
  public int MINIMUM_INSERT_SIZE

• MAXIMUM_INSERT_SIZE

  @Argument(shortName="MAX_INS",
            doc="The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
  public int MAXIMUM_INSERT_SIZE

• INCLUDE_NON_PF_READS

  @Argument(shortName="NON_PF",
            doc="Whether or not to include non-PF reads.")
  public boolean INCLUDE_NON_PF_READS

• USE_OQ

  @Argument(doc="When available, use original quality scores for filtering.")
  public boolean USE_OQ

• CONTEXT_SIZE

  @Argument(doc="The number of context bases to include on each side of the assayed G/C base.")
  public int CONTEXT_SIZE

• CONTEXTS

  @Argument(doc="The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.",
            optional=true)
  public Set<String> CONTEXTS

• STOP_AFTER

  @Argument(doc="For debugging purposes: stop after visiting this many sites with at least 1X coverage.")
  public int STOP_AFTER

Constructor Detail

• CollectOxoGMetrics

  public CollectOxoGMetrics()

Method Detail

• requiresReference

  protected boolean requiresReference()

  Overrides:

  requiresReference in class CommandLineProgram

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Description copied from class: CommandLineProgram
  Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

  Overrides:

  customCommandLineValidation in class CommandLineProgram

  Returns:

  null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

• doWork

  protected int doWork()

  Description copied from class: CommandLineProgram
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

  Specified by:

  doWork in class CommandLineProgram

  Returns:

  program exit status.